References

Model-based drug development: a rational approach to efficiently accelerate drug development

10.1038/clpt.2013.54 · 2013 · External reference

Computational oncology--mathematical modelling of drug regimens for precision medicine

10.1038/nrclinonc.2015.204 · 2016 · External reference

Systems biology in drug discovery

10.1038/nbt1017 · 2004 · External reference

Computational modeling of mammalian signaling networks

10.1002/wsbm.52 · 2010 · External reference

BlotIt-optimal alignment of western blot and qPCR experiments

10.1371/journal.pone.0264295 · 2022 · External reference

Quantitative live-cell imaging and computational modeling shed new light on endogenous WNT/CTNNB1 signaling dynamics

10.7554/elife.66440 · 2021 · External reference

Live cell analysis and mathematical modeling identify determinants of attenuation of Dengue Virus 2’-O-Methylation Mutant

10.1371/journal.ppat.1005345 · 2015 · External reference

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

2018 · External reference

Temporal and spatial topography of cell proliferation in cancer

10.1038/s41556-022-00860-9 · 2022 · External reference

The structure of the human cell cycle

10.1016/j.cels.2021.10.007 · 2022 · External reference

Advances in high-throughput mass spectrometry in drug discovery

10.15252/emmm.202114850 · 2023 · External reference

Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing

10.1038/s41592-021-01153-z · 2021 · External reference

High-throughput and high-sensitivity full-length single-cell RNA-seq analysis on third-generation sequencing platform

10.1038/s41421-022-00500-4 · 2023 · External reference

scPerturb: harmonized single-cell perturbation data

10.1038/s41592-023-02144-y · 2024 · External reference

Diffusion pseudotime robustly reconstructs lineage branching

10.1038/nmeth.3971 · 2016 · External reference

Visualizing structure and transitions in high-dimensional biological data

10.1038/s41587-019-0336-3 · 2019 · External reference

Reconstructing cell cycle pseudo time-series via single-cell transcriptome data

10.1038/s41467-017-00039-z · 2017 · External reference

PHATE: a dimensionality reduction method for visualizing trajectory structures in high-dimensional biological data

2017 · External reference

CellRank for directed single-cell fate mapping

10.1038/s41592-021-01346-6 · 2022 · External reference

CellRank 2: unified fate mapping in multiview single-cell data

10.1038/s41592-024-02303-9 · 2024 · External reference

LineageOT is a unified framework for lineage tracing and trajectory inference

10.1038/s41467-021-25133-1 · 2021 · External reference

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

2019 · External reference

Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells

2024 · External reference

Unresolved reference

2022 · External reference

Untangling biological factors influencing trajectory inference from single cell data

2020 · External reference

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

10.1038/s41467-019-09670-4 · 2019 · External reference

Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle

10.1038/nature11897 · 2013 · External reference

Trajectories of cell-cycle progression from fixed cell populations

10.1038/nmeth.3545 · 2015 · External reference

Circular trajectory reconstruction uncovers cell-cycle progression and regulatory dynamics from single-cell Hi-C maps

10.1002/advs.201900986 · 2019 · External reference

Universal prediction of cell-cycle position using transfer learning

10.1186/s13059-021-02581-y · 2022 · External reference

Models in biology: lessons from modeling regulation of the eukaryotic cell cycle

10.1186/s12915-015-0158-9 · 2015 · External reference

Modeling the cell cycle: why do certain circuits oscillate?

10.1016/j.cell.2011.03.006 · 2011 · External reference

Temporal self-organization of the cyclin/Cdk network driving the mammalian cell cycle

10.1073/pnas.0903827106 · 2009 · External reference

A model for restriction point control of the mammalian cell cycle

10.1016/j.jtbi.2004.04.039 · 2004 · External reference

Computational systems biology of the cell cycle

10.1093/bib/bbp005 · 2009 · External reference

A data-driven, mathematical model of mammalian cell cycle regulation

2014 · External reference

A skeleton model for the network of cyclin-dependent kinases driving the mammalian cell cycle

10.1098/rsfs.2010.0008 · 2011 · External reference

Pharmacodynamic modeling of cell cycle effects for gemcitabine and trabectedin combinations in pancreatic cancer cells

10.3389/fphar.2016.00421 · 2016 · External reference

Modelling of the cancer cell cycle as a tool for rational drug development: a systems pharmacology approach to cyclotherapy

10.1371/journal.pcbi.1005529 · 2017 · External reference

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method

10.1038/ncomms9390 · 2015 · External reference

Parameter estimation in models of biological oscillators: an automated regularised estimation approach

10.1186/s12859-019-2630-y · 2019 · External reference

Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints

10.1186/s12918-016-0319-7 · 2016 · External reference

Unresolved reference

External reference

Cyclin-dependent kinases and cell-cycle transitions: does one fit all?

10.1038/nrm2510 · 2008 · External reference

RNA velocity unraveled

10.1371/journal.pcbi.1010492 · 2022 · External reference

Unresolved reference

2022 · External reference

Positive feedback keeps duration of mitosis temporally insulated from upstream cell-cycle events

10.1016/j.molcel.2016.09.018 · 2016 · External reference

Patterns of cell cycle checkpoint deregulation associated with intrinsic molecular subtypes of human breast cancer cells

10.1038/s41523-017-0009-7 · 2017 · External reference

Role of cyclin B1/Cdc2 up-regulation in the development of mitotic prometaphase arrest in human breast cancer cells treated with nocodazole

2011 · External reference

Palbociclib-mediated cell cycle arrest can occur in the absence of the CDK inhibitors p21 and p27

10.1098/rsob.210125 · 2021 · External reference

G(1) and G(2) cell-cycle arrest following microtubule depolymerization in human breast cancer cells

10.1172/jci13275 · 2002 · External reference

Structural, enzymatic and spatiotemporal regulation of PP2A-B55 phosphatase in the control of mitosis

10.3389/fcell.2022.967909 · 2022 · External reference

Protein phosphatase 1 is essential for Greatwall inactivation at mitotic exit

10.15252/embr.201540876 · 2015 · External reference

APC/C(Cdc20) controls the ubiquitin-mediated degradation of p21 in prometaphase

10.1016/j.molcel.2007.06.013 · 2007 · External reference

Deubiquitylation and stabilization of p21 by USP11 is critical for cell-cycle progression and DNA damage responses

10.1073/pnas.1714938115 · 2018 · External reference

Progress of CDK4/6 inhibitor palbociclib in the treatment of cancer

10.2174/1871521409666170412123500 · 2018 · External reference

A fast algorithm to assess local structural identifiability

10.1016/j.automatica.2015.05.004 · 2015 · External reference

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood

10.1093/bioinformatics/btp358 · 2009 · External reference

Growth factors can influence cell growth and survival through effects on glucose metabolism

10.1128/mcb.21.17.5899-5912.2001 · 2001 · External reference

Insulin-like growth factor-I accelerates the cell cycle by decreasing G1 phase length and increases cell cycle reentry in the embryonic cerebral cortex

10.1523/jneurosci.3246-04.2004 · 2004 · External reference

Nonlinear mixed-effects modelling for single cell estimation: when, why, and how to use it

10.1186/s12918-015-0203-x · 2015 · External reference

Nonlinear mixed-effects models for modeling in vitro drug response data to determine problematic cancer cell lines

10.1038/s41598-019-50936-0 · 2019 · External reference

Quantitative examination of five stochastic cell-cycle and cell-size control models for Escherichia coli and Bacillus subtilis

10.3389/fmicb.2021.721899 · 2021 · External reference

A comprehensive review of computational cell cycle models in guiding cancer treatment strategies

10.1038/s41540-024-00397-7 · 2024 · External reference

Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle

10.1063/1.3677190 · 2012 · External reference

Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing

10.1016/j.cels.2024.07.002 · 2024 · External reference

The molecular architecture of cell cycle arrest

10.15252/msb.202211087 · 2022 · External reference

Cell-type-specific signaling networks in heterocellular organoids

10.1038/s41592-020-0737-8 · 2020 · External reference

Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop

10.1038/s41467-022-34536-7 · 2022 · External reference

Unresolved reference

2023 · External reference

Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle

10.1038/nature11897 · 2013 · External reference

Constitutive expression of E2F-1 leads to p21-dependent cell cycle arrest in S phase of the cell cycle

10.1038/sj.onc.1207571 · 2004 · External reference

p21 in cancer: intricate networks and multiple activities

10.1038/nrc2657 · 2009 · External reference

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems

10.1093/bioinformatics/btv405 · 2015 · External reference

Lessons learned from quantitative dynamical modeling in systems biology

10.1371/journal.pone.0074335 · 2013 · External reference